Ok, here is a list of the best pokemon and their moves.

Swampert: surf, earthquake, ice beam, hyper beam
Rayquaza: ice beam, outrage, flamethrower, thunderbolt

Salamence: dragon claw, fly, crunch, flamethrower
Kyogre: surf, ice beam, thunderbolt, water spout
Jirachi: thunderbolt, return, doom desire, thunder
Gorebyss: psychic, hydro pump, surf, ice beam

Yes, Kyogre CAN learn thunderbolt, just use TM 24, found at the game corner.

I have NEVER lost with this party, even in link battles.